Three-dimensional (3D) bioprinting technology is one of the most advanced techniques currently applied in tissue engineering and regenerative medicine and has developed rapidly in the past few years. Despite many breakthroughs, there are still several challenges of 3D bioprinting technology awaiting to be addressed, and one of them is the urgency of optimizing bioinks (natural or synthetic hydrogel), which are critical elements in 3D bioprinting, for specific properties. Different from traditional hydrogels, microgels, which are a new type of bioink, are micron-sized gels with excellent mechanical and biological properties, which make them great candidates for applications in 3D bioprinting. Different from the dense and limited pore size of traditional hydrogels, the pore structure of microgel is adjustable, enabling better cell loading before 3D bioprinting, and the printed pores are conducive to the exchange of metabolic substances and cell migration. The "bottom-up" modular microgel has stronger customizable characteristics, and it can freely adjust its mechanical properties, such as hardness, toughness, and rheological properties. In this review, we review the application of microgels in the field of biomedicine and discuss the future development of microgels in 3D bioprinting.